Inflammation is the foundation for cancer and degenerative/autoimmune diseases. Small changes in diet and exercise, e.g. omega-3 oils, vitamin D, low starch, and maintaining muscle mass, can dramatically alter predisposition to disease and aging, and minimize the negative impact of genetic risks. Based on my experience in biological research, I am trying to explain how the anti-inflammatory diet and lifestyle combat disease. 190 more articles at http://coolinginflammation.blogspot.com

Anti-Inflammatory Diet

All health care starts with diet. My recommendations for a healthy diet are here:

Friday, July 25, 2014

The medical industry is slowly pulling away from diet advice that has contributed significantly to disease in America. It promoted or at least tolerated, the shift from butter to margarine and polyunsaturated vegetable oils, and from saturated fats in meats to starches and grains. The medical emissary, Dr. Oz, still supports medical advice that is not based on medical research.

Dr. Oz's Five Food Felons and Why His Choices Are Unhealthy:

"1) Trans fats raise lousy LDL cholesterol and triglyceride levels, lower your healthy HDL cholesterol level and fuel disease-triggering inflammation." Trans fats are inflammatory and should not be eaten. New labeling has permitted substantial amounts of trans fats to be added to processed foods and still be labelled "No trans fats." LDL blood levels reflect inflammation, but artificially lowering the LDL with statins has no impact on heart disease. Lowering LDL, by lowering inflammation with fish oil and/or repair of gut flora, diet and exercise is effective.

"2)Saturated fat in red meats, poultry skin, full-fat dairy products and palm and coconut oils fuels cancer risk, coronary artery disease, dementia, obesity and diabetes." Linking saturated fats with heart disease, etc. was never supported by medical research. Elimination of red meat, removing skin from chicken, avoiding egg yolks, etc. and replacing them with omega-6 polyunsatured vegetable oils has been a major contributor to inflammation and disease. Full fat milk is the healthful choice, especially for children. The change was dangerous and is being reversed with new emphasis placed on omega-3 fish oils.

"3)Added sugars and 4) sugar syrups cause the proteins in your body to be less functional and age your immune and cardiovascular systems and your joints. Plus, they disrupt your metabolism and contribute to almost every lifestyle-related malady, including some cancers." Oz got this right even though they initially promoted high fructose corn syrup (half glucose/oligos) and its evil and even higher fructose sister agave nectar (all fructose/oligos.) Equally bad, however, are the hyperglycemic starch in breads (including whole grain!) and over cooked pasta.

Gut flora

"5)Refined and processed grains don't contain the fiber or nutrients (contained in 100 percent whole grains) that you need to keep the bacteria in your guts happy, glucose levels regulated, immune system strong and digestion running smoothly." Dr. Oz and company fail to understand the basics of vitamins, soluble fiber and gut flora. Grains are not healthy for most people, because of the toxicity of gluten and hyperglycemic starch. Ultra fine milling and fast commercial bread making eliminate the resistant starch. "Whole grain" processed foods just add back the insoluble fiber that is considered toxic, because of its phytic acid content. Grains should just be replaced with whole foods, such as vegetables that contain the soluble fiber that feeds the gut flora that provide all of the needed vitamins and are required for immune system development.

Why Does Dr. Oz Make Health Mistakes?

Dr. Oz has been criticized for promoting foods, supplements, medical treatments, etc. that are not supported by medical research. While that is true, I think that he is just following the general views of the medical industry and simply doesn't know any better. Sadly, most doctors don't have the background to read scientific research papers, let alone their own biomedical literature that is rife with scandals of nonreproducibility and inappropriate industry influence. Doctors find it hard to give valid dietary advice, because nutritionists have false information and celebrity doctors, and their research teams, don't do their homework. The result is the mix of ancient orthodoxy, industry promotion, alternative medicine and unscientific fads that appears in the media. Doctors need a scientific background sufficient to answer the essential question posed to health claims, "Does it make sense?"

56 comments:

Anonymous
said...

Hey, not sure if there will be a good thread to post this in, so I wanted to put up some results I got from the anti-inflammatory diet.

I'm basically doing the anti-inflammatory diet as posted, with the exception that I probably eat more bread and brown rice and such than you'd recommend. (If I don't get enough carbs, I feel it for sure in my exercises). Still, I've lowered my intake of them.

I also adopted a couple things from Animal Pharm. I take 2 TBsp potato starch + 1 TBsp psyllium husk power mid-morning fasted. (I practice intermittent fasting). Along with that I've been taking 2 capsule of AOR Probiotic 3 and 1 tablet of Prescript Assist probiotic (less than the full dosage). I get another two TBsp of potato starch in the afternoon mixed with a protein shake. (I use Protein 17, which claims to have one and only ingredient: whey protein from organically raised cows fed with organically raised grass).

I also take Viva Labs Krill Oil daily along with some additional supplements and exercise hard regularly.

Additionally, I follow more or less the "just eat real food" model of avoiding processed junk. I also regularly eat kimchi (which I get home made from various Korean groceries) and raw kraut. I try not to wash my farmers market veggies before eating.

First, the diet plan is easy. The worst part of paleo and a more "straight edge" AID is eliminating grains. That's one reason I don't do it. I want something that's long term sustainable for me and life without bread isn't that. The only real "challenge" product is mayo. I make my own from olive and coconut oil and it's not hard at all - and delicious I might add. I think as long as you don't go too crazy with trying to eliminate grains, this is very easy to integrate into a regular lifestyle. In fact, it's actually easier and tastier in many cases. No more fat free yogurt or skinny lattes. Lots of well marbled steaks. I'm self-employed, however, so have more flexibility than your average guy.

Second, I've noticed a number of health benefits. Among them are reduced allergy symptoms. I've long had low grade allergies pretty much year round, especially a bit of a runny nose, which is obnoxious and makes me prone to colds. I'll have to see if this holds up longer term or is actually a seasonal issue, but this has lessened a lot. Also, I had some mild psoriasis that has all but disappeared.

I have a bit of mild rosecea that I haven't seen any change in, but I noticed previous posts here suggest that's a challenging one.

I haven't noticed any colds which may be from better immune system and also from the reduced allergy symptoms.

I also had somewhat dry eyes that now seem normal. My mother actually tipped me that fish oil did it the same for her, so I attribute this to the krill oil. Not sure if this is inflammation related or not.

In short, three months in I see some tangible results in chronic health annoyances in my life.

The only negative I've observed is definitely increased gas problems with the resistant starch that has not subsided. I'm not sure what to do about this. It's new so can't be related to things I ate previously.

I have one strong caution to note. Dr. BG at Animal Pharm has spoken fondly of bentonite clay. I decided I'd try 30 days of it when I started the program figuring, "Even if it's a gimmick, what's the harm?" I took one teaspoon daily first thing am with nothing to eat until lunch except my mid-morning potato starch/psyllium drink. One thing I thought is that since this thing supposedly binds metals, it might help break up any magnesium biofilms in my gut. I'm not sure if it had that effect, but it did appear to bind magnesium alright as I developed symptoms of magnesium deficiency while taking this. I think I've long been magnesium deficient, but this really caused issues I attribute to a severe deficiency. As soon as I finished the bentonite and started supplementing with 400mg magnesium citrate daily, my symptoms went away. In short, from my personal experience perspective, bentonite clay is, shall we say, highly contraindicated.

Oh, one last thing. I've had larger and more regular bowel movements as well. What's more, I haven't had a single episode of diarrhea since being on this. Generally at least once a month something I eat would trigger some kind of GI reaction. But not on the anti-inflammation diet, the aforementioned gas excepted.

Here's an amusing Dr. Oz story. My friend needed a valve replacement and was told the best surgeons were Oz and Bill Clinton's surgeon. She chose Clinton's. On the day of the operation, while lying on a gurney having been prepped for surgery, alone in a small room, the door suddenly opened and Oz strode in. He ignored her and made a beeline for a mirror hanging on the wall, ran his hand over his hair, and walked out.

Anna,I think that colostrum may be useful for infection therapy, but not for daily use. Like whey, colostrum is adapted to eliminate adult gut flora and support infant flora (dairy probiotics) on mother's milk. I don't think that there is a reasonable case to support the routine use of any supplements, especially most vitamins. They should all be seen as therapeutic until the cause is cured.

In most cases, even with genetic predispositions, disease can be avoided or remedied with diet, adapted gut flora, sleep and exercise. No supplements needed.

This study highlights an important aspect of bacterial metabolites & their role in determining a suitable 'milieu' for themselves as well as for our own cells.The experiment appears relatively well controlled & carried out. It presents the 'butyrate paradox' in an interesting way.I understood this as being strongly suggestive that we should seek an appropriate dynamic equilibrium between us & our bacteria rather than follow "the > fiber, the better because of > butyrate".

Essentially, if the problem with classical ANTIbiotics is their indiscriminate killing of the wrong bacterial species then surely PRE/PRObiotics can also suffer from the same indiscriminancy - fuelling the wrong bacterial species as well.

- “Butyrate has been shown to have antiproliferative and anticancer properties, likely through its action as an HDACi. However, at lower concentrations, butyrate stimulates colon epithelial cell proliferation”

- “The discrepancy on the effects of butyrate on CRC has been termed the ‘‘butyrate paradox.’”

- “butyrate has been shown to modulate canonical Wnt signaling, and depending on the status of b-catenin activity, colon epithelial cells respond differently to butyrate”

Butyrate concentration differs in proximal / distant colon, and its significantly lower deep in the crypts, where the neoplasmatic cells are formed. TOO LITTLE butyrate does not inhibit proliferation of a tumour cell, it is rather used up as fuel. Increase butyrate, and the proliferation is inhibited. Especially increase butyrate content at the distal part of the colon, where most of the colorectal cancer starts. (No, it won’t happen by eating more butter).Haven’t you already heard it here?

In other words, if there is already a tumour cell at the bottom of the crypt and there is too little butyrate reaching it, there is no inhibition.

“Butyrate is an attractive candidate for chemotherapy or chemoprevention because it selectively inhibits tumor growth and has minimal adverse effects in clinical trials (Pouillart, 1998). However, the efficacy of butyrate as a chemotherapeutic agent has been limited by its rapid uptake and metabolism by normal cells (resulting in a half-life of 6 min and peak blood levels below 0.05 mM [Miller et al., 1987]) before reaching tumors (Pouillart, 1998). More stable butyrate derivatives such as tributyrin have also not been successful on a consistent basis (Pouillart, 1998). A fiber-rich diet might be more successful for chemoprevention because it delivers mM levels of butyrate (via the microbiota) to the correct place (the colon) before the onset or at an early stage of tumorigenesis. Evidence for this idea comes from recent human studies demonstrating lower levels of butyrate-producing bacteria among the gut microbiota of colorectal cancer patients compared to healthy participants (Balamurugan et al., 2008; Wang et al., 2012), and studies showing an inverse correlation between fecal butyrate levels and tumor size in colorectal cancer (Boutron-Ruault et al., 2005; Monleón et al., 2009).”

Our body really likes its fat. It likes it so much, it uses carbohydrates to fulfill a lot of the same functions fat does (& vice-versa?).Redundancy & mechanistic diversity is a true evolutionary treat.

- Astrocytes & "neurons within the brain preserve information by their continued existence. This is best done by burning LACTATE or KETONES. NOT glucose and, of course, not FFAs" [Peter@Hyperlipid; http://high-fat-nutrition.blogspot.nl/2014/07/in-comments-following-previous-post.html]

It seems to me that a ketogenic diet*/LCHF with a diverse & plentiful intake of fibres from fruit/veg/animal tissues would likely satisfy all 3 criteria just mentioned (or gets us closer to them, at least).

*ketogenic in the sense that ones metabolism is good at living off its fat - **but which might accommodate for a 'substantial' amount of absorbable dietary carbs [your mileage may vary]

Gemma and Raphi,I think that you have provided a balanced discussion of the essential role of butyrate and SCFAs in colon health. I would also like to add that there should be an expectation of a high level of variability in SCFA production in response to fermentable fiber, dependent on the composition of the gut flora. In the previous article, I simplistically assigned a role to SCFA uptake in the colon to obesity. The articles here indicate very low serum levels of butyrate. But what actually happens in obese mice? Obesity and obese gut flora are a risk factor for CRC. Does that mean that the colon is exposed to high or low butyrate in obesity and CRC?

-"there should be an expectation of a high level of variability in SCFA production in response to fermentable fiber, dependent on the composition of the gut flora"--> my point exactly Dr.Ayers. In principle, adding more of the 'right' fuel (butyrate) to wrong 'thing' (particular bacterial species) is a potential pitfall which (IMHO) should be reflected in our fiber/pre/probiotic recommendations.

This MAY also explain some of the contradictory epidemiology (fiber is positively & negatively associated with colon cancer) & weak clinical data (fiber has a positive effect, but it's rarely significant or too variable for practical applications).

- "But what actually happens in obese mice?"--> "microbiota increase metabolic efficiency in the host" & so "despite this increased food intake, GF mice are leaner than CONV-R controls and are resistant to obesity induced by a high-fat diet*"[not a healthy human HF diet, but a vegetable oil laden bag o' cr^p]

- "Does that mean that the colon is exposed to high or low butyrate in obesity and CRC?"--> according to Donohoe "colonic tissue derived from GF mice exhibited diminished NADH/NAD+ ratios and ATP levels as compared to colonic tissue derived from CONV-R mice" ...furthermore, they "demonstrated that butyrate rescues a severe deficit in oxidative metabolism in GF colonocytes. However, we were surprised that glucose did not compensate for the lack of butyrate in GF colonocytes"It appears like colonocytes can have an ATP deficit for > 1 reason.

Our strictly 'human' metabolism APPEARS more comfortable producing the most ATP units per turn of the TCA cycle...& bacteria are happy to grant our colonocytes the same treatment - all we have to do is feed them things we can't break down & ta-da! Butyrate it is!

But how do you feed something that isn't there? Or how do you find A rather than B? I think sequenced elimination & reintroduction (of all kind of drugs & plants) will prove very important in future therapies.

Anon,I found that article interesting, but I still have trouble with the concept of hormesis, that eating a little of toxic phytochemicals is healthy because it turns on the body's detox system.

The evidence seems to be that eating plants with phytoalexins improves health by some measure. Unfortunately, purified phytochemicals do not provide the same health benefit. This suggests that it wasn't actually the phytochemicals that were beneficial, but rather some other plant component, such as the polysaccharides = soluble fiber.

There is also the example of plants in which breeding programs have focused on lowering the toxicity of the phytochemicals. That results in plants that are more palatable, which we find in the supermarket, but also need more pesticides and herbicides. Some of those domesticated plants have been modified experimentally to produce more protective and toxic phytochemicals to make them cheaper to grow, but unfortunately that reduces yields. The implication is that eating minimal amounts of phytochemicals would be beneficial, because it would provide protection against inflammation-based ROS. Unfortunately, it would also have metabolic costs and potentially other unintended health costs.

Thus, small amounts of plant polyphenolic, anti-oxidant phytoalexins might be beneficial, but none would be better.

I am not saying that we should avoid eating plants, which are inherently toxic, but rather that we should be aware that we need to be healthy to tolerate them and that they are not healthy for fetuses or young children with undeveloped detox systems. Children naturally nurse for several years, because breast milk is safer and healthier than adult food or processed formula.

Thank you, Dr. Ayers. For ten years I have been trying to improve my nutrition by adding a scoop of whey protein every morning. What confusion I must have created in my gut when I started following my whey protein smoothie with a sauerkraut chaser.

I recall you saying a while ago that you consumed dairy for pleasure, not for health. I should have paid more attention. Now, I think I’ve got it.

I think that we should point out one other aspect of fermentation. Butyrate fermentation starts with pyruvate and high energy electrons on NADH, and ends up with ATP, butyrate and NAD. That's just as in other fermentation pathways and oxidative phosphorylation in mitochondria. My point is that butyrate can't be metabolize further in the anaerobic colon, but it can be used in the oxygenated mitochondria of colonocytes.

In cattle the excess butyrate from antibiotic treatment results in fatty steaks. Is it the same for fatty thighs in humans? Is there a major metabolic shift in gut flora as a contributor of obesity? Is it as stated that calories are the cause of obesity or is it the distribution of calories between absorbed butyrate vs. conversion to more gut flora/feces?

Anon,I quoted all five of Oz's food felons and I agreed with trans fats being an unnecessary, predatory product that the food industry persists in using despite its health risk. I also took the opportunity to comment on Dr. Oz's confusion about the biomedical literature, which clearly shows that statins lower LDL, but lower LDL is not healthful, and the actual issue is inflammation that is better treated with inexpensive fish oil and exercise.

You have mentioned here amd there ,in connection with microbiome health, that you shoulden't eat too many different foods. I have been pondering that idea. And if I understand you correctly, the idea is that our microbiome changes rapidly in response to diet, and too much variation might cause some unwanted imbalances.

So along with SAD diets, PUFAS, GMO and ABX, the ubiquitiy of various cuisines. Ight be another contributor to our national ill health.

So, if that is indeed what you are saying, I would love to hear more details of how much variation is too much. What kind of things should we not vary too much? And are there others i which we have. Ore leeway.

I might add that this whole concept is appealiing to me from the point of view of simplifying my life in terms of meal planning and helping to declutter my house by clealing out my kitchen cupboards.

Dr Ayers, I wanted to alert you this book and webpage regarding pot belly syndrome...visceral fat...and gut health. The premise is that the bacteria Chlamydophila pneumoniae – which is abbreviated CPN. CPN belongs to a class of germs sometimes referred to as middle-path germs.

"CPN Infections Lead to a POT BELLY SYNDROME (PBS)

"As the CPN-infected host gets progressively sicker, their inflammatory response escalates. Too much inflammation can harm the host, so the body attempts to counter-regulate this mounting inflammation with an adrenal hormone called cortisol. As the illness lingers on, more and more cortisol is pumped out by the sick host’s adrenal glands. The result mimics Cushing’s syndrome – a disease produced by a benign adrenal tumor that over-secretes cortisol. Excess cortisol causes weight gain, central obesity, fatigue, diabetes, depression, insomnia, and irritability to name just a few of the more salient symptoms of this syndrome.PBS closely resembles Cushing’s syndrome and has been described as Metabolic Syndrome X with elevated cortisol levels. The increasing waist line, high blood pressure, high serum glucose, and the high blood lipids of Syndrome X develop in the presence of ongoing inflammation, fatigue, stress, mounting malnutrition. It is the rare physician that suspects that a persistent middle-path germ like CPN is acting as a silent terrorist inciting the genesis of the Potbelly Syndrome!"

Several months ago you gave us the name and author of a book on fermentation that was going to be published in August. Now I cannot find the information and would like to purchase a copy when it is available. Would you give that info again, please.

I have questions about fermentation that I cannot find the answer to elsewhere—for example: is it necessary to ferment a variety of veggies or can I get the bacteria I need from just sauerkraut? Or, sauerkraut fermented a shorter length of time tastes better (in my estimation) but do you get more helpful bacteria if it is fermented for a longer period of time?

Totally off topic,You can go to the author's websiteFermentista.us and she has a write up of her new book. Also Sandor Katz has some great books about fermentation. Another website I follow is Phickle.com

I will let the good doctor answer your question about length of fermentation and bacteria.

please could you comment on this work cited by Ray Peat on starch.I'm afraid it might apply to resistant starch as well, which could irritate the bowel.

"Volkheimer (in the 1960s) found that mice fed raw starch aged at an abnormally fast rate, and when he dissected the starch-fed mice, he found a multitude of starch-grain-blocked arterioles in every organ, each of which caused the death of the cells that depended on the blood supplied by that arteriole. It isn’t hard to see how this would affect the functions of organs such as the brain and heart, even without considering the immunological and other implications of the presence of foreign particles randomly distributed through the tissue."http://raypeat.com/articles/nutrition/carrageenan.shtml

I need some advice! About 4 years ago I radically changed my diet - I was basically eating everything from a box before. Then I started cooking and eating organic veggies and fruit, using olive oil, real butter, grass-fed beef, etc. I also started eating lots of grains/ seeds and baking using GF flours (lots of almond flour) with agave nectar and honey.

A year after that, I started to have lots of tartar /plaque buildup behind on my lower teeth and my dentist thought it was a hygiene issue. Which was not the case because I would brush/ floss after every meal. I spent years seeing several other dentists, but nothing changed. I started to look into the possibility that it may be diet related, which led me to Weston Price, and ultimately to your website.

I've also experienced constipation issues. And looking back on it now, the mild allergies I had to dogs/ cats increased after my diet change, but I'm only now seeing the possible connection to diet/ gut /allergies.

I very recently stopped consuming any grains/seeds and switched to the anti-inflammatory diet entirely. I took a probiotic and have been taking vit-k and consuming full fat-yogurt along with fish oil I've been taking for years.

I'm wondering if I should take some type of laxative to rid bad biofilms and start building a healthy gut, or if what I'm doing now is enough? I'm also wondering how long it would take to build healthy gut flora? I also don't have a gall badder, so I'm wondering about my body's ability to breakdown fats and thus absorb fat soluble vitamins is drastically affected and if I should alter my diet because of that.

I like many people came across your website as I am currently going through a case of acute diffuse uveitis. My Rheumy believes that I might have mild Ankylosing Spondylitis and my GI beleives I might have some inflammatory bowel diseases too. Since the underlying causes all seem to be inflammation related, I am trying to get this under control.

I was on a Ketogenic diet since 5/12 primarily for weight loss. I have been a life long vegetarian (with my ancestors over 5-6 generations being vegetarians as well). However, since I found it difficult to stay vegetarian, I started adding meat, primarily burgers. I am a 32 yr Male South Asian Indian who lived on primarily rice based diet for 27 years. About 2 weeks after I started eating meat, I started getting this high inflammation symptoms such as uveitis, joint and back pains and it is still ongoing. I am on oral prednisone which controls the symptoms till it is time for my next dose.

DO you think I might have lost (or never had) gut flora that could process meat in the first place. If yes, how do I recover this back. Will fermented veggies and Kefir help me with processing meat? Or would you suggest I stay vegetarian for now.

There is a lot of information in the website that I am trying hard to get to an actionable plan. For now, I am cutting down on meats. Primarily staying on tofu stir fry, boca burgers and cauliflower rice. Hopefully the phytoestrogens in Tofu might help ?

For supplements, I take Vitamin D, Turmeric and Fish Oil and GSM. Is there anything else I should be using in your opinion.

I understand that there might be additional information in the blog posts and I will continue to go through them. But any information in the meanwhile could be very helpful.

Kiran,I can only try to explain what is happening to support your medical treatment and of course, I cannot give you medical advice.

A healthy diet has needed protein and fats, but also soluble fiber in vegetables to feed gut flora. A vegan or low carb paleo diet, to include the extremes and everything in between, can be healthy, but only with soluble fiber to which the gut flora are adapted. All diets without corresponding, adapted gut flora are unhealthy.

In your case, I assume that you inherited a diet along with adapted gut flora. Unfortunately, you probably damaged your gut flora with antibiotics, or altered diet, prior to shifting to burgers lacking in soluble fiber and that was the end of the gut bacteria that control the development of the suppressive half of the immune system in your gut. The result is autoimmune disease attacking autoantigens in many parts of your body.

Since healthy gut bacteria supply all of the vitamins one needs, your damaged gut flora will also leave you vitamin deficient. Your chronic inflammation will also block your ability to produce vitamin D in your skin using sun light. You need to test your serum vit.D, supplement and retest until it is in the high range.

Resistant starch/potato starch and soil based probiotics containing Clostridium is now the typical recommendation for repairing gut flora to support treatment for autoimmune diseases. I wrote several posts on RS. It took years for you to get in your current immunocompromised position, so it will also take months to repair your immune system.

You might also mention Metformin to your healthcare team. Many people with your symptoms also had viral infections that were activated by dietary shifts.

I would say that being strict vegetarian or not is unimportant. I would return to the veggies that you previously ate and focus on providing enough soluble fiber to feed, what you hope are, remnants of your previous gut flora. You also need live fermented foods and other sources of bacteria to recolonized your damaged gut flora. Check out the Anti-Inflammatory Diet that I recommend on my blog to eliminate inflammatory vegetable oils, etc.

Val,I think that you should start by spending some time going over a few of my 200+ posts that provide the answers to your questions as well as your problems. You give me the impression that I am more concerned and spend more time fixing your health, than you do.

Your problems clearly result from dysbiosis, yet you just change your diet, when the major target is fixing your gut flora.

Agave nectar? You must be kidding. Why would anyone think that an industrial sweetener that is pure fructose, high fructose corn syrup on steroids, would be healthy?

I have discussed constipation as a symptom of severe dysbiosis ad nauseum. You need new bacteria. Changing your diet can provide soluble fiber to feed bacteria to make poop, but diet cannot create new bacteria. You have killed off all but a few species of your gut bacteria. Think of clear cutting a forest and growing just corn and soybeans. Then you decide that you want a forest again after hundreds of species are extinct. That is constipation, extinct gut flora. You have to eat bacteria to poop bacteria. Nothing grows in a fertilized and watered garden, except weeds (pathogens), unless you add seeds (normal gut bacteria, from soil based probiotics, fermented food, "muddy" veggies, etc.)

Thanks Dr. Art. That was very helpful. I understand you cannot give medical advice. I have to help myself, and you are doing a great service that provides a foundation for me and people like me to get started off on.

I have started working on a plan to include more fiber. I will be adding more RS. You mention soluble fiber, but don't specifically mention Psyllium supplements. I was under the impression that they are soluble fiber as well. Does psyllium help in any way at all? A search on your blog does not bring up any hits.

I am also getting upto speed on fermented foods and will be working on growing homemade/fermented foods. I also am getting some prebiotic supplements containing Clostrdium.

I realized that my ketogenic diet was pretty similar to the anti inflammation diet that you mentioned. However, what left me scratching my head was why would my inflammation act up when I was in a diet that supposedly controls it. Your website is the only one that came close to providing an answer (though I am not qualified to judge it) suggesting that diet and gut bacteria should match.

I hope I see some improvement without having to be put on Immunosuppresants.

Kiran,I don't understand why you are asking about soluble fiber supplements, when what you need are the naturally occurring soluble fiber you were eating in the form of vegetables prior to your burger binges.

You need soluble fiber that can be digested, i.e. has the genes for enzymes to hydrolyze, by bacteria already present in your gut. Otherwise, you need to add soluble fiber, e.g. resistant starch, and bacteria with the right enzymes, in that case, Clostridium butyricum from Probiotics3.

Psyllium is used as a laxative, because until you develop gut flora to digest it, the partial digestion products irritate your gut and cause minor diarrhea, which people think is fixing their constipation. It is just causing a new series of compensating symptoms.

In your case, you have an half of your immune system wiped out or suppressed. You are half immunosuppressed, leaving only the aggressive half to rampage. The doctors want to fix your symptoms by wiping out the remaining half of your immune system to make you fully incompetent and therefor unable to mount autoimmune attacks.

The Anti-inflammatory Diet that I recommend removes the vegetable fats and high carbs that contribute to diet-based inflammation. It doesn't address the contributions of gut flora based disruption of the immune system, that is the other big factor in inflammation. So the anti-inflammatory diet merely revealed your underlying gut flora dysfunction. Also drop the ketogenic diet nomenclature, since it never applied, if you were following a diet similar to mine. A true ketogenic diet would be useful therapeutically in other cases, but only temporarily, and not for autoimmune diseases. I wouldn't consider it to be Paleo, for example.

I discovered your blog a week ago and I've read a ton of your posts. I was just wondering if I had really destroyed the gut flora and if I had to go the laxative route to fix it.

The diet I listed was the diet I changed from eating box food to real food - just me wanting to be healthier, not based on those health concerns I listed which occurred after the change. I'm not saying agave was healthy, but at the time {very early 20s} I thought it was healthier and baking in general was healthier than the way I was eating {little debbie, chip ahoy}.

I've been trying to fix my teeth issues for years with my parents, dr and dentist all making me think I'm crazy to even think it could be connected to diet. I've had lab work, gone to several dentists. Yes, this is all very new to me but I've been reading and trying to process as much as I can in the last week.

What I concluded was to take a PEG based laxative to clear my gut and then take vinegar and eat apples and probiotics to help repair it. And ongoing full fat yogurt would be helpful too. And not to eat a wide variety of food. Plus partially washed fresh veggies, plus fermented food. That's me breaking it down simply for myself.

I talked to my dr and there seems to be no way to get golytely to clear me out. So I was wondering if there is an alternative laxative? One that has worked for others that is over the counter?

I apologize if it came off as if I'm not concerned with my health, as I am very much and really was hopeless until I found your blog. I'm just trying to stop the damage as fast as possible and only right NOW it seems like I've found another soul that is saying "it is connected to diet, you're not crazy."

Also - I had read your post -"Constipation, Gut Flora and Health" and the comments where you said:

"I think that using probiotics should also be paired with trying to change to healthy gut flora using an anti-inflammatory diet, such as the one I outline on this blog. The probiotics taken a little at a time may have a continued effect, but a good dose of live yogurt (without the sucrose/HFCS) is just as good, if not better. I haven't seen any comparison studies. "

And that's why I asked if what I was doing now was enough. Because I'm not sure exactly where to begin, in all honesty.

Others have suggested being scoped or a colon cleanse would be good options to start with. But that's why I wrote what I did about my situation, to get specific steps for myself. As I started doing what you suggested above and it was implied that I hadn't read your articles based on what I said I did, which was what you had suggested in some comments. I am really trying to figure this out and not get discouraged in the process.

Should you need it, MiraLAX is a PEG (Polyethylene Glycol 3350) laxative available OTC. Amazon.com offers it. I do wish you well in your pursuit of improved health/diet. There's a lot to learn from this site! Many thanks to Dr. Ayers for his efforts. Best, KM

Medical research and the recommendations which emanate from their conclusions change over time. Biochemical, genetic, epignetic and psycho-social-spiritual uniquenss make evidence based medicine good at determining the utility of interventions for population as a whole. However, the recommendations only offer probabilities of efficacy for speicific interventions in any individual. So, in fact there is no one diet which is good for every one. My best diet is fish, rice and salads. My wife's is root veggies, limited protein, lots of fat; Therefore, there are some logical things that one can do to be healthy. Test your sense of well being (measure over a 2 week period for each test) with various dietary habits. Work on increasing happiness (sense of meaning and efficacy-see Amrtin Seligman's work), and if you can, strive for continuous awareness of some higher power that makes sense to you; this will help your adrenal stress response system normalize its steroid output, which helps chronic inflammation; Use herbs such as turmeric or unflame herbal to naturally reduce inflammation (via TNF alpha receptor stabilization, and NF-Kappa B stabilization, which reduce cytokine production) All of this, perhaps with the help a coach or even better a friend who is targeting the some health problem, will make a very significant change in how you feel--and very quickly. Unflame works in hours to 1 day, turmeric in about 7 days, diet in 1-2 weeks, and stress reduction techniques over weeks to months of practice. Hope this helps.

Dr Art- Wondering your thoughts on the significance of strep in various stool cultures. on both ubiome and American gut, I had about 10X more strep than the "normal" population. also, had a genova test that showed large amounts of "alpha hemolytic and gamma heamolytic streptococcus". trying to address ongoing diarrhea/gas and not seeing much improvement from everything I've tried (including your suggestions) and others. thanks in advance!

Not a new article but new to mehttp://rhnegativebloodsecrets.blogspot.ca/2013/01/are-you-related-to-neanderthals.html

I'm hlab27+ with AS and anterior uveitis.

Do you think that certain people are genetically MORE susceptible to specific bacterial/fungal/microbial/viral/ parasitic infections? I would think timing, nutritionally, stress-wise and lack of exercise, would help open the door wider for those infections in the same people. My question is: Is it possible that certain "bloodlines"/genetic traits leave us without the proper defense mechanisms for certain infections which in turn lead to autoimmunity, as opposed to having a genetic predisposition to autoimmunity itself?

I had a synovial tissue sample test positive for C.Trachomatis. Based on the results, my integrative Dr. recommends I get off immunosuppressants and start with this protocol;6 months rifampin + 6 months azithromycin.

Dr. Grace Lui forwarded through this article but I'm not sure what an acceptable level of C. Trachomatis is, if any?http://www.ncbi.nlm.nih.gov/pubmed/15972529

As a side note, my friend had a pneumonnial infection and got psoriasis one month after. My Father was battling a fungal infection and now has a mysterious form of, what has been labelled for now, a severe auto immune issue.

Probably all questions that won't be answered for quite some time but I'd love to know your opinions.

I should add that I would attempt to break down and irradicate biofilms and candida before starting the protocol http://www.townsendletter.com/June2012/candida0612.html

and concurrently follow a no offending foods diet. I wonder if tons of dirty organic veggies, sbo's, RS and a one month long series of FMT's would bring the rainforest back to life after complete clear cutting and deforestation?

Hi everybody. Can anyone suggest to me a practitioner I could work with who follows Dr. Ayers' protocols? I know there are a number of GAPS practitioners out there, so perhaps there is someone I could work with who is in line with these suggestions? Maybe someone who can perform stool tests to determine which bacteria are missing, and help me with particulars of how to replace them? I am trying to help my child.

I did the gut repair steps with the PEG that you outlined in a post on constipation (PEG, natto, re-upping with pro- pre- biotics, etc)

How will I know if everything is good to go? I'm wondering if I should do it once a week for a month, or if once is enough? I imagine it will take time to rebuild the proper gut bacteria, so I am wondering about the time frame or some signs that I am heading in the right direction.

Environmentally induced alterations in the commensal microbiota have been implicated in the increasing prevalence of food allergy. We show here that sensitization to a food allergen is increased in mice that have been treated with antibiotics or are devoid of a commensal microbiota. By selectively colonizing gnotobiotic mice, we demonstrate that the allergy-protective capacity is conferred by a Clostridia-containing microbiota. Microarray analysis of intestinal epithelial cells from gnotobiotic mice revealed a previously unidentified mechanism by which Clostridia regulate innate lymphoid cell function and intestinal epithelial permeability to protect against allergen sensitization. Our findings will inform the development of novel approaches to prevent or treat food allergy based on modulating the composition of the intestinal microbiota.

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About Me

I grew up in San Diego and did my PhD in Molecular, Cellular and Developmental Biology (U. Colo. Boulder). I subsequently held postdoctoral research positions at the Swedish Forest Products Research Laboratories, Stockholm, U. Missouri -Colombia and Kansas State U. I was an assistant professor in the Cell and Developmental Biology Department at Harvard University, and an associate professor and Director of the Genetic Engineering Program at Cedar Crest College in Allentown, PA. I joined the faculty at the College of Idaho in 1991 and in 1997-98 I spent a six-month sabbatical at the National University of Singapore. Most recently I have focused on the role of heparin in inflammation and disease.